Contacts of the strand formed by residues 136 - 142 (chain B) in PDB entry 1KY9
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101B VAL* 4.2 16.2 - - + -
102B THR 3.5 2.2 - - - +
104B ASN* 4.0 2.1 - - - +
131B ASP 3.0 26.8 + - - +
134B SER* 3.2 30.5 + - - +
135B ASP* 1.3 77.0 - - - +
137B ALA* 1.3 65.3 - - - +
224B ILE* 3.8 32.1 - - + -
226B THR* 6.4 0.2 - - - -
242B ILE* 3.7 27.4 - - + -
247B VAL* 4.3 16.2 - - + -
250B LEU* 4.2 17.0 - - + -
251B THR* 5.3 3.8 - - - +
254B MSE 3.4 12.4 - - + +
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Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B VAL* 3.5 5.7 - - - +
102B THR* 2.6 47.7 + - + +
103B ASN 4.2 1.3 - - - -
104B ASN* 3.9 8.5 - - - -
107B VAL* 3.7 28.7 - - + -
129B GLY 3.5 13.5 - - - +
130B LYS* 3.9 9.0 - - + +
136B ILE* 1.3 76.5 - - - +
138B LEU* 1.3 61.0 + - - +
251B THR* 5.6 0.2 - - - -
254B MSE 4.3 3.1 - - - -
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ILE* 5.1 4.0 - - + -
99B TYR* 4.2 16.4 - - + -
100B VAL 3.0 37.5 - - - +
101B VAL* 3.8 6.3 - - + +
127B MSE 4.0 0.5 - - - +
128B VAL* 3.1 36.8 + - + +
129B GLY 2.8 16.2 + - - +
137B ALA* 1.3 72.3 - - - +
139B ILE* 1.3 73.9 + - - +
251B THR* 3.3 29.2 - - + +
254B MSE 3.7 17.6 - - + -
255B VAL* 3.9 27.8 - - + -
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ILE* 3.9 17.9 - - + -
99B TYR* 3.4 6.1 - - - -
100B VAL* 2.8 52.0 + - + +
102B THR* 4.4 5.4 - - + -
107B VAL* 4.3 21.1 - - + -
113B ILE* 3.6 32.5 - - + -
115B VAL* 3.8 11.7 - - + -
125B ALA* 3.8 11.0 - - + -
126B LYS 3.4 14.8 - - - +
127B MSE 4.4 13.0 - - + -
128B VAL* 3.4 4.7 - - - -
138B LEU* 1.3 86.3 - - - +
140B GLN* 1.3 61.9 + - - +
141B ILE 5.8 0.2 - - - +
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Residues in contact with GLN 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LYS* 2.9 40.5 - - - +
98B GLY 3.1 1.3 - - - +
99B TYR* 3.4 32.8 + - + -
125B ALA* 3.2 4.9 - - - -
126B LYS* 3.0 34.8 + - + +
128B VAL* 4.5 7.2 - - + +
139B ILE* 1.3 74.4 - - - +
141B ILE* 1.3 68.8 + - - +
142B GLN* 3.2 14.4 + - - +
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Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ILE* 4.6 5.4 - - + -
97B LYS 4.4 1.4 - - - +
98B GLY* 2.7 21.5 + - - +
100B VAL* 3.9 26.0 - - + -
115B VAL* 4.5 22.0 - - + -
117B LEU* 4.6 7.9 - - + -
123B PHE* 3.4 44.0 - - + -
124B ASP 3.4 4.9 - - - -
125B ALA* 4.3 2.0 - - + -
140B GLN* 1.3 79.2 - - - +
142B GLN* 1.3 65.5 + - - +
143B ASN 3.4 2.4 + - - -
144B PRO* 3.6 19.1 - - + +
147B LEU* 3.6 28.7 - - + -
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Residues in contact with GLN 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B PHE* 3.9 6.4 - - - -
124B ASP* 2.5 39.2 + - + +
125B ALA* 4.3 0.2 - - - -
126B LYS* 3.2 46.8 - - + +
140B GLN* 3.3 27.4 + - - +
141B ILE* 1.3 78.5 - - - +
143B ASN* 1.3 81.0 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il